Organization and Format

Editorial Style

The editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2019, in-house document [you may find the ASM Word List helpful]) and How To Write and Publish a Scientific Paper, 7th ed. (Greenwood, Santa Barbara, CA, 2011), as interpreted and modified by the editors and the ASM Journals Department.

The editors and the Journals Department reserve the privilege of editing manuscripts to conform with the stylistic conventions set forth in the aforesaid publications and in these Instructions. Please note that ASM uses the serial comma.

On receipt at ASM, an accepted manuscript undergoes an automated preediting, cleanup, and tagging process specific to the particular article type. To optimize this process, manuscripts must be supplied in the correct format and with the appropriate sections and headings.

Type every portion of the manuscript double-spaced (a minimum of 6 mm between lines), including figure legends, table footnotes, and references, and number all pages in sequence, including the abstract, figure legends, and tables. Place the last two items after the References section. Manuscript pages should have line numbers; manuscripts without line numbers may be editorially rejected by the editor, with a suggestion of resubmission after line numbers are added. The font size should be no smaller than 12 points. It is recommended that the following sets of characters be easily distinguishable in the manuscript: the numeral zero (0) and the letter “oh” (O); the numeral one (1), the letter “el” (l), and the letter “eye” (I); and a multiplication sign and the letter “ex” (x). Do not create symbols as graphics or use special fonts that are external to your word processing program; use the “insert symbol” function. Set the page size to 8.5 by 11 inches (ca. 21.6 by 28 cm). Italicize any words that should appear in italics, and indicate paragraph lead-ins in boldface type. Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language.

Manuscripts may be editorially rejected, without review, on the basis of poor English or lack of conformity to the standards set forth in these Instructions.

Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language or engage a professional language editing service for help.

Supplemental Material

Supplemental material intended for posting by JVI should be restricted to large or complex data sets. Such material may include data from microarray, genomic, structural, proteomic, or video imaging analyses. In such cases, the manuscript submitted for review should include a distillation of the results so that the principal conclusions are fully supported without referral to the supplemental material.

Supplemental material will be peer reviewed along with the manuscript and must be uploaded to the eJournalPress (eJP) peer review system at initial manuscript submission. The decision to publish the material online with the accepted article is made by the editor. It is possible that a manuscript will be accepted but that the supplemental material will not be.

Supplemental material should be consolidated into a single file, if possible. If more than one file is necessary, the total number of supplemental material files is limited to 10. No supplemental material should be included in the main manuscript. Supplemental files should be submitted in the following standard formats.

Movies (Audio Video Interleave [.avi], QuickTime [.mov], or MPEG files) should be submitted at the desired reproduction size and length and should be accompanied by a legend. The maximum file size is 20 MB.

Movie legends should be uploaded in a single PDF file. The maximum file size is 8 MB.

Unlike the manuscript, supplemental material will not be edited by the ASM Journals staff and proofs will not be made available. References related to supplemental material only should not be listed in the References section of an article; instead, include them with the supplemental material. Supplemental material will always remain associated with its article and is not subject to any modifications after publication.

Material that has been published previously (print or online) is not acceptable for posting as supplemental material. Instead, the appropriate reference(s) to the original publication should be made in the manuscript.

Copyright for the supplemental material remains with the author, but a license permitting posting by ASM is included in the copyright transfer agreement completed by the corresponding author. If you are not the copyright owner, you must provide to ASM signed permission from the owner that allows posting of the material, as a supplement to your article, by ASM. You are responsible for including in the supplemental material any copyright notices required by the owner.

Research Articles

Research Articles should include the elements described in this section.

Title, running title, byline, affiliation line(s), and corresponding author. Each manuscript should present the results of an independent, cohesive study; thus, numbered series titles are not permitted. Exercise care in composing a main title. Avoid the main title/subtitle arrangement, complete sentences, and unnecessary articles. On the title page, include the title, the running title (not to exceed 54 characters and spaces), the name of each author, all authors' affiliations at the time the work was performed, the name(s) and e-mail address(es) of the corresponding author(s), and a footnote indicating the present address of any author no longer at the institution where the work was performed. Place a number sign (#) in the byline after the affiliation letter(s) of the author to whom inquiries regarding the paper should be directed (see "Correspondent footnote" below). Indicate each author's affiliation with a superscript lowercase letter placed after the author's surname in the byline (separate multiple affiliation letters with commas but no space). Each affiliation should have its own line and its own superscript affiliation letter preceding it. Do not consolidate different departments at one institution into one address with a single affiliation letter, even if all affected authors belong to all of those departments. Please review this sample title page for guidance.

Also include on the title page the word count for the abstract and the word count for the text (excluding the references, table footnotes, and figure legends).

Study group in byline. A study group, surveillance team, working group, consortium, or the like (e.g., the Active Bacterial Core Surveillance Team) may be listed as a coauthor in the byline if its contributing members satisfy the requirements for authorship and accountability as described on ASM Journals' Authorship page. The names (and institutional affiliations, if desired) of the contributing members may be given as a separate paragraph in Acknowledgments.

If the contributing members of the group associated with the work do not fulfill the criteria of substantial contribution to and responsibility for the paper, the group may not be listed in the author byline. Instead, it and the names of its contributing members may be listed in the Acknowledgments section.

Correspondent footnote. The e-mail address for the corresponding author should be included on the title page of the manuscript. This information will be published in the article as a footnote to facilitate communication and will be used to notify the corresponding author of the availability of proofs and, later, of the PDF file of the published article. No more than two authors may be designated corresponding authors.

Two-part abstract. Research Articles have structured abstracts consisting of two sections with their own headings: “Abstract” and “Importance.” Because the structured abstract will be published separately by abstracting services, it must be complete and understandable without reference to the text. Please refer to the sample structured abstract for guidance.

The Abstract section should be no more than 250 words and should concisely summarize the basic content of the paper without presenting extensive experimental details.

The Importance section should be no more than 150 words and should provide a nontechnical explanation of the significance of the study to the field. Avoid abbreviations and references, and indicate the specific organism under study. When it is essential to include a reference, use the format shown under “References” below (see the “Citations in abstracts” section).

Introduction. The introduction should supply sufficient background information to allow the reader to understand and evaluate the results of the present study without referring to previous publications on the topic. The introduction should also provide the hypothesis that was addressed or the rationale for the present study. Use only those references required to provide the most salient background rather than an exhaustive review of the topic.

Results. In the Results section, include the rationale or design of the experiments as well as the results; reserve extensive interpretation of the results for the Discussion section. Present the results as concisely as possible in one of the following: text, table(s), or figure(s). Data in tables (e.g., cpm of radioactivity) should not contain more significant figures than the precision of the measurement allows. Illustrations (particularly photomicrographs and electron micrographs) should be limited to those that are absolutely necessary to show the experimental findings. Number figures and tables in the order in which they are cited in the text, and be sure to cite all figures and tables.

Discussion. The Discussion should provide an interpretation of the results in relation to previously published work and to the experimental system at hand and should not contain extensive repetition of the Results section or reiteration of the introduction. In short papers, the Results and Discussion sections may be combined.

Materials and Methods. The Materials and Methods section should include sufficient technical information to allow the experiments to be repeated. When centrifugation conditions are critical, give enough information to enable another investigator to repeat the procedure: make of centrifuge, model of rotor, temperature, time at maximum speed, and centrifugal force (× g rather than revolutions per minute). For commonly used materials and methods (e.g., media and protein concentration determinations), a simple reference is sufficient. If several alternative methods are commonly used, it is helpful to identify the method briefly as well as to cite the reference. For example, it is preferable to state "cells were broken by ultrasonic treatment as previously described (9)" rather than to state "cells were broken as previously described (9)." This allows the reader to assess the method without constant reference to previous publications. Describe new methods completely, and give sources of unusual chemicals, equipment, and microbial strains. When large numbers of microbial strains or mutants are used in a study, include tables identifying the immediate sources (i.e., sources from whom the strains were obtained) and properties of the strains, mutants, bacteriophages, and plasmids, etc. Parameters such as temperature, pH, and salinity (or conductivity) must be reported for environmental samples that are extracted for molecular analyses.

A method or strain, etc., used in only one of several experiments reported in the paper may be described in the Results section or very briefly (one or two sentences) in a table footnote or figure legend. It is expected that the sources from whom the strains were obtained will be identified.

As noted on ASM Journals' Ethics Resources and Policies page, a paragraph dedicated to new accession numbers for nucleotide and amino acid sequences, microarray data, protein structures, gene expression data, and MycoBank data should appear at the end of Materials and Methods with the paragraph lead-in "Data availability." Please also provide references (with URLs) for the accession numbers.

Acknowledgments. Statements regarding sources of direct financial support (e.g., grants, fellowships, and scholarships, etc.) should appear in the Acknowledgments. A funding statement indicating what role, if any, the funding agency had in your study (for example, “The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.”) may be included. Funding agencies may have specific wording requirements, and compliance with such requirements is the responsibility of the author. In cases in which research is not funded by any specific project grant, funders need not be listed, and the following statement may be used: “This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.” Statements regarding indirect financial support (e.g., commercial affiliations, consultancies, stock or equity interests, and patent-licensing arrangements) are also allowed. It is the responsibility of authors to provide a general statement disclosing financial or other relationships that are relevant to the study.

Recognition of personal assistance should be given in the Acknowledgments section, as should any statements disclaiming endorsement or approval of the views reflected in the paper or of a product mentioned therein.

In addition to acknowledging sources of financial support in the manuscript, authors should list any sources of funding, in response to the Funding Sources question on the online submission form, providing relevant grant numbers where possible, and the authors associated with the specific funding sources. In the event that your submission is accepted, the funding source information provided in the submission form may be published, so please ensure that all information is entered accurately and completely. (It will be assumed that the absence of any information in the Funding Sources fields is a statement by the authors that no support was received.)

Appendixes. Appendixes that contain additional material to aid the reader but that would be cumbersome and inhibit understanding if placed in the main text are permitted. Titles, authors, and reference sections that are distinct from those of the primary article are not allowed. If it is not feasible to list the author(s) of the appendix in the byline or the Acknowledgments section of the primary article, rewrite the appendix so that it can be considered for publication as an independent article. Equations, tables, and figures should be labeled with the letter “A” preceding the numeral to distinguish them from those cited in the main body of the text. If they are vital to a reader understanding the paper, they should be incorporated into the manuscript as regular equations, tables, and figures.

References. In the reference list, references are numbered in the order in which they are cited in the article (citation-sequence reference system). In the text, references are cited parenthetically by number in sequential order. Data that are not published or not peer reviewed are simply cited parenthetically in the text (see section ii below).

(i) References listed in the References section. The following types of references must be listed in the References section:

Provide the names of all the authors and/or editors for each reference; long bylines should not be abbreviated with “et al.” All listed references must be cited in the text. Abbreviate journal names according to the PubMed Journals Database (National Library of Medicine, National Institutes of Health; available at https://www.ncbi.nlm.nih.gov/sites/entrez?db=journals), the primary source for ASM style. Do not use periods with abbreviated words. The EndNote output style for ASM Journals’ current reference style can be found at https://endnote.com/style_download/american-society-for-microbiology-asm-journals-2/; save it to your EndNote Styles folder (it should replace any earlier output styles for ASM journals [all ASM journals use the same reference style]). Note that DOIs are not needed for most references. ASM copy editors will automatically insert DOIs on all references in the CrossRef and PubMed databases during copyediting. URLs for government reports and other references not indexed in these databases should be provided if desired; URLs for citations of database accession numbers and code/software should be provided by you.

Falagas ME, Kasiakou SK. 2006. Use of international units when dosing colistin will help decrease confusion related to various formulations of the drug around the world. Antimicrob Agents Chemother 50:2274–2275. (Letter.) {“Letter” or “Letter to the editor” is allowed but not required at the end of such an entry.}

*A reference to an in-press ASM publication should state the control number (e.g., JVI00123-19) if it is a journal article or the name of the publication if it is a book.

In some online journal articles, posting or revision dates may serve as the year of publication, and a DOI (preferred) or URL is required for articles with nontraditional page numbers or electronic article identifiers.

Other journals may use different styles for their publish ahead-of-print manuscripts, but citation entries must include the following information: author name(s), posting date, title, journal title, and volume and page numbers and/or DOI. The following is an example:

To encourage data sharing and reuse, ASM recommends reporting data sets and/or code both in a dedicated “Data availability” paragraph and in References. The components of a complete data citation include the following:

responsible party (senior author, collector, agency),

publication year,

complete name of a data set, including the name of the database or repository and its URL, or the name of the analysis software (if appropriate), including the version and project,

Manuscript submissions that have appeared in preprint archives should cite the preprint in References, and the fact that a paper has appeared online before should be mentioned parenthetically at the end of the introductory section: (This article was submitted to an online preprint archive [1].) The reference should take the form noted above in reference 18.

(ii) References cited in the text. References that should be cited in the text include the following:

Unpublished data

Manuscripts submitted for publication

Unpublished conference presentations (e.g., a report or poster that has not appeared in published conference proceedings)

Personal communications

Patent applications and patents pending

Computer software, databases, and websites (home pages)

These references should be made parenthetically in the text as follows:

URLs for companies that produce any of the products mentioned in your study or for products being sold may not be included in the article. However, company URLs that permit access to scientific data related to the study or to shareware used in the study are permitted.

(iii) Citations in abstracts. Since the abstract must be able to stand apart from the article, references cited in it should be clear without recourse to the References section. Use an abbreviated form of citation, omitting the article title, as follows.

This style should also be used for references cited in legends for supplemental material and in Addenda in Proof.

(iv) References related to supplemental material. If references must be cited in the supplemental material, list them in a separate References section within the supplemental material and cite them by those numbers; do not simply include citations of numbers from the reference list of the associated article. If the same reference(s) is to be cited in both the article itself and the supplemental material, then that reference would be listed in both References sections.

Gems

Gems are brief invited reviews (limited to 4,000 words) on a current topic or emerging story in virology. The aim is to publish cogent summaries of key findings and new developments written clearly and succinctly for the broad virology community. Gems should also include a discussion of the importance of the new findings in advancing the field and may include opinions and views on future directions. Gems should include one or two figures or tables. The abstract is limited to 75 words. Gems are solicited by JVI associate editors. Authors may propose topics to the associate editors, who will select the topics and invite submissions. Unsolicited Gems will not be considered.

Minireviews

Minireviews are brief (limit of 6,000 words, exclusive of references) summaries of important developments in virology research. They must be based on published articles and may address any subject within the scope of the journal.

Minireviews are solicited by the Minireview editors and are subject to review. Unsolicited reviews will not be considered. Ideas for Minireviews may be sent to the Minireview editors. Manuscripts should be submitted via the eJP online manuscript submission and peer review system.

Minireviews must have abstracts. Limit the abstract to 250 words or fewer. The body of the Minireview may have section headings and/or paragraph lead-ins.

Author Bios

At the editor’s invitation, corresponding authors of Minireviews may submit a short biographical sketch and photo for each author for publication with the article. Biographical information should be submitted at the modification stage.

The text limit is 150 words for each author and should include WHO you are (your name), WHERE you received your education, WHAT positions you have held and at WHICH institutions, WHERE you are now (your current institution), WHY you have this interest, and HOW LONG you have been in this field.

The photo should be a black-and-white head shot of passport size. Photos will be reduced to approximately 1.125 inches wide by 1.375 inches high. Photos must meet the production criteria for regular figures and should be checked for production quality by using Rapid Inspector, provided at the following URL: http://rapidinspector.cadmus.com/RapidInspector/zmw/index.jsp.

To submit, upload the text and photos with your modified manuscript in the eJP online manuscript submission and peer review system. Include the biographical text after the References section of your manuscript, in the same file. Upload the head shots in the submission system as a “Minireview Bio Photo”; include the author’s name or enough of it for identification in each photo’s file name.

Commentaries

Commentaries are invited communications concerning topics relevant to the readership of JVI and are intended to engender discussion. Reviews of the literature, methods and other how-to papers, and responses targeted at a specific published paper are not appropriate. Commentaries are subject to review.

The length may not exceed 3,000 words, and the format is like that of a Minireview (see above) except that the abstract is limited to 75 words.

Letters to the Editor

Two types of Letters to the Editor may be submitted. The first type (Comment Letter) is intended for comments on final, typeset articles published in the journal (not on accepted manuscripts posted online) and must cite published references to support the writer's argument. The second type (New-Data Letter) may report new, concise findings that are not appropriate for publication as Research Articles.

Letters may be no more than 500 words long and must be typed double-spaced. Refer to a recently published Letter for correct formatting. Note that authors and affiliations are listed below the title.

All Letters to the Editor must be submitted electronically, and the type of Letter (New Data or Comment) must be selected from the choices in the submission form. For Letters commenting on published articles, the cover letter should state the volume and issue in which the article was published, the title of the article, and the last name of the first author. Letters to the Editor do not have abstracts. Both types of Letter must have a title, which must appear on the manuscript and on the submission form. Figures and tables should be kept to a minimum.

If the Letter is related to a published article, it will be sent to the editor who handled the article in question. The letter will be sent for peer review. If the editor believes that publication is warranted, he/she will solicit a reply from the corresponding author of the article and make a recommendation to the editor in chief. Final approval for publication rests with the editor in chief.

New-Data Letters will be assigned to an editor according to subject matter and will be sent for peer review by that editor. After review, the editor will send a recommendation to the editor in chief. Final approval for publication rests with the editor in chief.

Please note that some indexing/abstracting services do not include Letters to the Editor in their databases.